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Lutz T, Langer GJ, Heinze C. A virus from Aspergillus cibarius with features of alpha- and betachrysoviruses. Virus Genes 2024; 60:71-79. [PMID: 38160229 PMCID: PMC10861612 DOI: 10.1007/s11262-023-02043-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 11/21/2023] [Indexed: 01/03/2024]
Abstract
From the ascomycete Aspergillus cibarius strain NW-FVA 2590, which was originally isolated from a root, associated with stem collar necrosis of Fraxinus excelsior L., a novel virus was isolated and characterized. Its genome is encoded on three monocistronic dsRNA segments ranging from 3683 bp (dsRNA 1) over 3093 (dsRNA 2) to 2902 bp (dsRNA 3), which are packed in isometric particles of around 35 nm. While the viral RdRp (P1) is encoded on segment 1, protein sequencing showed that two more structural proteins are present which are translated from dsRNA 2 (P2) and dsRNA 3 (P3) and possibly form the viral capsid. Additionally, P2 and P3 may undergo posttranslational modifications since the detected proteins bands deviated from the calculated sizes. Due to its phylogenetic position, the novel virus was grouped in the family of Chrysoviridae and was tentatively denominated as Aspergillus cibarius chrysovirus 1 (AcCV1). Due to its composition, biological properties and phylogenetic position, distant from the genera Alphachrysovirus and Betachrysovirus, we suggest to position AcCV1 in a proposed genus "Gammachrysovirus".
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Affiliation(s)
- Tobias Lutz
- Institute of Plant Science and Microbiology, University of Hamburg, Molecular Phytopathology, Ohnhorststr. 18, 22609, Hamburg, Germany
| | - Gitta Jutta Langer
- Nordwestdeutsche Forstliche Versuchsanstalt, Grätzelstr. 2, 37079, Göttingen, Germany
| | - Cornelia Heinze
- Institute of Plant Science and Microbiology, University of Hamburg, Molecular Phytopathology, Ohnhorststr. 18, 22609, Hamburg, Germany.
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Hough B, Steenkamp E, Wingfield B, Read D. Fungal Viruses Unveiled: A Comprehensive Review of Mycoviruses. Viruses 2023; 15:1202. [PMID: 37243288 PMCID: PMC10224137 DOI: 10.3390/v15051202] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/07/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023] Open
Abstract
Mycoviruses (viruses of fungi) are ubiquitous throughout the fungal kingdom and are currently classified into 23 viral families and the genus botybirnavirus by the International Committee on the Taxonomy of Viruses (ICTV). The primary focus of mycoviral research has been on mycoviruses that infect plant pathogenic fungi, due to the ability of some to reduce the virulence of their host and thus act as potential biocontrol against these fungi. However, mycoviruses lack extracellular transmission mechanisms and rely on intercellular transmission through the hyphal anastomosis, which impedes successful transmission between different fungal strains. This review provides a comprehensive overview of mycoviruses, including their origins, host range, taxonomic classification into families, effects on their fungal counterparts, and the techniques employed in their discovery. The application of mycoviruses as biocontrol agents of plant pathogenic fungi is also discussed.
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Affiliation(s)
| | | | - Brenda Wingfield
- Forestry & Agricultural Biotechnology Institute (FABI), Department of Biochemistry, Genetics & Microbiology, University of Pretoria, Pretoria 0002, South Africa; (B.H.); (E.S.); (D.R.)
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3
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Ayllón MA, Vainio EJ. Mycoviruses as a part of the global virome: Diversity, evolutionary links and lifestyle. Adv Virus Res 2023; 115:1-86. [PMID: 37173063 DOI: 10.1016/bs.aivir.2023.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Knowledge of mycovirus diversity, evolution, horizontal gene transfer and shared ancestry with viruses infecting distantly related hosts, such as plants and arthropods, has increased vastly during the last few years due to advances in the high throughput sequencing methodologies. This also has enabled the discovery of novel mycoviruses with previously unknown genome types, mainly new positive and negative single-stranded RNA mycoviruses ((+) ssRNA and (-) ssRNA) and single-stranded DNA mycoviruses (ssDNA), and has increased our knowledge of double-stranded RNA mycoviruses (dsRNA), which in the past were thought to be the most common viruses infecting fungi. Fungi and oomycetes (Stramenopila) share similar lifestyles and also have similar viromes. Hypothesis about the origin and cross-kingdom transmission events of viruses have been raised and are supported by phylogenetic analysis and by the discovery of natural exchange of viruses between different hosts during virus-fungus coinfection in planta. In this review we make a compilation of the current information on the genome organization, diversity and taxonomy of mycoviruses, discussing their possible origins. Our focus is in recent findings suggesting the expansion of the host range of many viral taxa previously considered to be exclusively fungal, but we also address factors affecting virus transmissibility and coexistence in single fungal or oomycete isolates, as well as the development of synthetic mycoviruses and their use in investigating mycovirus replication cycles and pathogenicity.
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Affiliation(s)
- María A Ayllón
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo, Pozuelo de Alarcón, Madrid, Spain; Departamento Biotecnología-Biología Vegetal, E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, Spain.
| | - Eeva J Vainio
- Forest Health and Biodiversity, Natural Resources Institute Finland (Luke), Helsinki, Finland
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Shahi S, Chiba S, Kondo H, Suzuki N. Cryphonectria nitschkei chrysovirus 1 with unique molecular features and a very narrow host range. Virology 2020; 554:55-65. [PMID: 33383414 DOI: 10.1016/j.virol.2020.11.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 11/21/2020] [Accepted: 11/23/2020] [Indexed: 12/20/2022]
Abstract
Cryphonectria nitschkei chrysovirus 1 (CnCV1), was described earlier from an ascomycetous fungus, Cryphonectria nitschkei strain OB5/11, collected in Japan; its partial sequence was reported a decade ago. Complete sequencing of the four genomic dsRNA segments revealed molecular features similar to but distinct from previously reported members of the family Chrysoviridae. Unique features include the presence of a mini-cistron preceding the major large open reading frame in each genomic segment. Common features include the presence of CAA repeats in the 5'-untranslated regions and conserved terminal sequences. CnCV1-OB5/11 could be laterally transferred to C. nitschkei and its relatives C. radicalis and C. naterciae via coculturing, virion transfection and protoplast fusion, but not to fungal species other than the three species mentioned above, even within the genus Cryphonectria, suggesting a very narrow host range. Phenotypic comparison of a few sets of CnCV1-infected and -free isogenic strains showed symptomless infection in new hosts.
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Affiliation(s)
- Sabitree Shahi
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046, Japan
| | - Sotaro Chiba
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046, Japan
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046, Japan.
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5
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Otulak-Kozieł K, Kozieł E, Escalante C, Valverde RA. Ultrastructural Analysis of Cells From Bell Pepper ( Capsicum annuum) Infected With Bell Pepper Endornavirus. FRONTIERS IN PLANT SCIENCE 2020; 11:491. [PMID: 32411163 PMCID: PMC7199235 DOI: 10.3389/fpls.2020.00491] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/01/2020] [Indexed: 05/05/2023]
Abstract
Endornaviruses include viruses that infect fungi, oomycetes, and plants. The genome of plant endornaviruses consists of linear ssRNA ranging in size from approximately 13-18 kb and lacking capsid protein and cell-to-cell movement capability. Although, plant endornaviruses have not been shown to cause detectable changes in the plant phenotype, they have been associated with alterations of the host physiology. Except for the association of cytoplasmic vesicles with infections by Vicia faba endornavirus, effects on the plant cell ultrastructure caused by endornaviruses have not been reported. Bell pepper endornavirus (BPEV) has been identified in several pepper (Capsicum spp.) species. We conducted ultrastructural analyses of cells from two near-isogenic lines of the bell pepper (C. annuum) cv. Marengo, one infected with BPEV and the other BPEV-free, and found cellular alterations associated with BPEV-infections. Some cells of plants infected with BPEV exhibited alterations of organelles and other cell components. Affected cells were located mainly in the mesophyll and phloem tissues. Altered organelles included mitochondrion, chloroplast, and nucleus. The mitochondria from BPEV-infected plants exhibited low number of cristae and electron-lucent regions. Chloroplasts contained plastoglobules and small vesicles in the surrounding cytoplasm. Translucent regions in thylakoids were observed, as well as hypertrophy of the chloroplast structure. Many membranous vesicles were observed in the stroma along the envelope. The nuclei revealed a dilation of the nuclear envelope with vesicles and perinuclear areas. The organelle changes were accompanied by membranous structure rearrangements, such as paramural bodies and multivesicular bodies. These alterations were not observed in cells from plants of the BPEV-free line. Overall, the observed ultrastructural cell alterations associated with BPEV are similar to those caused by plant viruses and viroids and suggest some degree of parasitic interaction between BPEV and the plant host.
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Affiliation(s)
- Katarzyna Otulak-Kozieł
- Institute of Biology, Department of Botany, Warsaw University of Life Sciences—SGGW, Warsaw, Poland
| | - Edmund Kozieł
- Institute of Biology, Department of Botany, Warsaw University of Life Sciences—SGGW, Warsaw, Poland
| | - Cesar Escalante
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
| | - Rodrigo A. Valverde
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
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Petrzik K, Koloniuk I, Sehadová H, Sarkisova T. Chrysoviruses Inhabited Symbiotic Fungi of Lichens. Viruses 2019; 11:v11121120. [PMID: 31817044 PMCID: PMC6949994 DOI: 10.3390/v11121120] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 11/26/2019] [Accepted: 11/30/2019] [Indexed: 12/28/2022] Open
Abstract
A lichen body is formed most often from green alga cells trapped in a net of ascomycetous fungi and accompanied by endolichenic or parasitic fungi, other algae, and symbiotic or free-living bacteria. The lichen’s microcosmos is inhabited by mites, insects, and other animals for which the lichen is a source of food or a place to live. Novel, four-segmented dsRNA viruses were detected in saxicolous Chrysothrixchlorina and Lepraria incana lichens. Comparison of encoded genome proteins revealed classification of the viruses to the genus Alphachrysovirus and a relationship to chrysoviruses from filamentous ascomycetous fungi. We propose the names Chrysothrix chrysovirus 1 (CcCV1) and Lepraria chrysovirus 1 (LiCV1) as acronyms for these viruses. Surprisingly, observation of Chrysothrix chlorina hybridization with fluorescent-labelled virus probe by confocal microscope revealed that the CcCV1 virus is not present in the lichen body-forming fungus but in accompanying endolichenic Penicilliumcitreosulfuratum fungus. These are the first descriptions of mycoviruses from a lichen environment.
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Affiliation(s)
- Karel Petrzik
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic; (I.K.); (T.S.)
- Correspondence: ; Tel.: +420-387-775-549
| | - Igor Koloniuk
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic; (I.K.); (T.S.)
| | - Hana Sehadová
- Institute of Entomology, Biology Centre, Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic;
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Tatiana Sarkisova
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic; (I.K.); (T.S.)
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Zhang T, Li N, Yuan Y, Cao Q, Chen Y, Tan B, Li G, Liu D. Blue-White Colony Selection of Virus-Infected Isogenic Recipients Based on a Chrysovirus Isolated from Penicillium italicum. Virol Sin 2019; 34:688-700. [PMID: 31376081 DOI: 10.1007/s12250-019-00150-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 05/14/2019] [Indexed: 11/29/2022] Open
Abstract
Mycoviruses have been found to infect more than 12 species of Penicillium, but have not been isolated from Penicillium italicum (P. italicum). In this study, we isolated and characterized a new double-stranded RNA (dsRNA) virus, designated Penicillium italicum chrysovirus 1 (PiCV1), from the citrus pathogen P. italicum HSPi-YN1. Viral genome sequencing and molecular characterization indicated that PiCV1 was highly homologous to the previously described Penicillium chrysogenum virus. We further constructed the mutant HSPi-YN1ΔpksP defective in the polyketide synthase gene (pksP), which is involved in pigment biosynthesis, and these mutants formed albino (white) colonies. Then we applied hyphal anastomosis method to horizontally transmit PiCV1 from the white virus-donors (i.e., HSPi-YN1 mutants) to wild-type recipients (i.e., P. italicum strains HSPi-CQ54, HSPi-HB4, and HSPi-HN1), and the desirable PiCV1-infected isogenic recipients, a certain part of blue wild-type strains, can be eventually selected and confirmed by viral genomic dsRNA profile analysis. This blue-white colony screening would be an easier method to select virus-infected P. italicum recipients, according to distinguishable color phenotypes between blue virus-recipients and white virus-donors. In summary, the current work newly isolated and characterized PiCV1, verified its horizontal transmission among dually cultured P. italicum isolates, and based on these, established an effective and simplified approach to screen PiCV1-infected isogenic recipients.
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Affiliation(s)
- Tingfu Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Na Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China.,Yunnan Higher Education Institutions, College of Life Science and Technology, Honghe University, Mengzi, 661199, China
| | - Yongze Yuan
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Qianwen Cao
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Yanfen Chen
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Binglan Tan
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Guoqi Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Deli Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China.
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Kartali T, Nyilasi I, Szabó B, Kocsubé S, Patai R, Polgár TF, Nagy G, Vágvölgyi C, Papp T. Detection and Molecular Characterization of Novel dsRNA Viruses Related to the Totiviridae Family in Umbelopsis ramanniana. Front Cell Infect Microbiol 2019; 9:249. [PMID: 31380294 PMCID: PMC6644447 DOI: 10.3389/fcimb.2019.00249] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 06/26/2019] [Indexed: 11/24/2022] Open
Abstract
Umbelopsis ramanniana is an oleaginous fungus belonging to the Mucoromycotina subphylum. Our group had previously detected four double-stranded RNA (dsRNA) bands in the U. ramanniana NRRL 1296 strain by gel electrophoresis. Here we describe the molecular characterization of its dsRNA elements as well as the discovery of four novel dsRNA viruses: Umbelopsis ramanniana virus 1 (UrV1), Umbelopsis ramanniana virus 2 (UrV2), Umbelopsis ramanniana virus 3 (UrV3), and Umbelopsis ramanniana virus 4 (UrV4). Full genomes of UrV1, UrV3, and UrV4 were determined using the full-length amplification of cDNAs (FLAC) technique; they contain two open reading frames (ORF), which putatively encode the coat protein (CP) and the RNA dependent RNA polymerase (RdRp), respectively. In case of UrV2, a partial ORF encoding a partial RdRp gene could be determined. Based on the phylogeny inferred from the RdRp sequences, UrV1 and UrV4 belong to the genus Totivirus, while UrV2 may belong to the genus Victorivirus. UrV3 nested to a novel, unclassified group of Totiviridae, which is related to the genus Totivirus. Hybridization analysis revealed that the dsRNA molecules of UrV1 and UrV4 correspond to the same 5.0-kbp electrophoretic band, whilst the probe for the UrV3 hybridized to the largest, 5.3-kbp and the 3.0-kbp bands of the dsRNA pattern of U. ramanniana. Interestingly, the probe for the UrV2 sequence did not hybridized to any dsRNA bands, but it could be amplified from the isolated 3.0-kbp fragment. By transmission electron microscopy, two different isometric virus particles with about 50 and 35 nm in diameter were detected in U. ramanniana NRRL 1296 indicating that this strain harbor multiple viruses. Beside U. ramanniana, dsRNA elements were also detected in other Umbelopsis isolates with different patterns consisting of 2 to 4 discrete and different sized (0.7–5.3-kbp) dsRNA molecules. Based on a hybridization analysis with UrV1 CP and RdRp probes, the bands with the size of around 5.0-kbp, which were present in all tested Umbelopsis strains, are presumed as possible full mycovirus genomes.
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Affiliation(s)
- Tünde Kartali
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Ildikó Nyilasi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Boglárka Szabó
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Sándor Kocsubé
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Roland Patai
- Biological Research Centre of the Hungarian Academy of Sciences, Institute of Biophysics, Szeged, Hungary
| | - Tamás F Polgár
- Biological Research Centre of the Hungarian Academy of Sciences, Institute of Biophysics, Szeged, Hungary
| | - Gábor Nagy
- MTA-SZTE Fungal Pathogenicity Mechanisms Research Group, Department of Microbiology, University of Szeged, Hungarian Academy of Sciences, Szeged, Hungary
| | - Csaba Vágvölgyi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Tamás Papp
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary.,MTA-SZTE Fungal Pathogenicity Mechanisms Research Group, Department of Microbiology, University of Szeged, Hungarian Academy of Sciences, Szeged, Hungary
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Wang S, Yang Z, Zhang T, Li N, Cao Q, Li G, Yuan Y, Liu D. Molecular Characterization of a Chrysovirus Isolated From the Citrus Pathogen Penicillium crustosum and Related Fungicide Resistance Analysis. Front Cell Infect Microbiol 2019; 9:156. [PMID: 31157173 PMCID: PMC6529537 DOI: 10.3389/fcimb.2019.00156] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 04/26/2019] [Indexed: 12/30/2022] Open
Abstract
Penicillium sp. are damaging to a range of foods and fruits including citrus. To date, double-stranded (ds)RNA viruses have been reported in most Penicillium species but not in citrus pathogen P. crustosum. Here we report a novel dsRNA virus, designated as Penicillium crustosum chrysovirus 1 (PcCV1) and isolated from P. crustosum strain HS-CQ15. PcCV1 genome comprises four dsRNA segments, referred to as dsRNA1, dsRNA2, dsRNA3, and dsRNA4, which are 3600, 3177, 3078, and 2808 bp in length, respectively. Sequence analysis revealed the presence of four open reading frames (ORFs) in the PcCV1 genome. ORF1 in dsRNA1 encodes a putative RNA-dependent RNA polymerase (RdRp) and ORF2 in dsRNA2 encodes a putative coat protein (CP). The two remaining ORFs, ORF3 in dsRNA3 and ORF4 in dsRNA4, encode proteins of unknown function. Phylogenetic analysis based on RdRp sequences showed that PcCV1 clusters with other members of the genus Chrysovirus, family Chrysoviridae. Transmission electron microscope (TEM) analysis revealed that the PcCV1 visions are approximately 40 nm in diameter. Regarding biological effects of PcCV1, HS-CQ15 harboring the chrysovirus exhibited no obvious difference in colony morphology under fungicide-free conditions but decreased resistance to demethylation inhibitor (DMI)-fungicide prochloraz, as compared to PcCV1-cured strain. Here we provide the first evidence of a virus present in citrus pathogenic fungus P. crustosum and the chrysovirus-induced change in fungicide-resistance of its host fungus.
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Affiliation(s)
- Shengqiang Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Zhu Yang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Tingfu Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Na Li
- College of Life Science and Technology, Honghe University, Mengzi, China
| | - Qianwen Cao
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Guoqi Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Yongze Yuan
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Deli Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
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10
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Nerva L, Vigani G, Di Silvestre D, Ciuffo M, Forgia M, Chitarra W, Turina M. Biological and Molecular Characterization of Chenopodium quinoa Mitovirus 1 Reveals a Distinct Small RNA Response Compared to Those of Cytoplasmic RNA Viruses. J Virol 2019; 93:e01998-18. [PMID: 30651361 PMCID: PMC6430534 DOI: 10.1128/jvi.01998-18] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 01/08/2019] [Indexed: 02/07/2023] Open
Abstract
Indirect evidence of mitochondrial viruses in plants comes from discovery of genomic fragments integrated into the nuclear and mitochondrial DNA of a number of plant species. Here, we report the existence of replicating mitochondrial virus in plants: from transcriptome sequencing (RNA-seq) data of infected Chenopodium quinoa, a plant species commonly used as a test plant in virus host range experiments, among other virus contigs, we could assemble a 2.7-kb contig that had highest similarity to mitoviruses found in plant genomes. Northern blot analyses confirmed the existence of plus- and minus-strand RNA corresponding to the mitovirus genome. No DNA corresponding to the genomic RNA was detected, excluding the endogenization of such virus. We have tested a number of C. quinoa accessions, and the virus was present in a number of commercial varieties but absent from a large collection of Bolivian and Peruvian accessions. The virus could not be transmitted mechanically or by grafting, but it is transmitted vertically through seeds at a 100% rate. Small RNA analysis of a C. quinoa line carrying the mitovirus and infected by alfalfa mosaic virus showed that the typical antiviral silencing response active against cytoplasmic viruses (21- to 22-nucleotide [nt] vsRNA peaks) is not active against CqMV1, since in this specific case the longest accumulating vsRNA length is 16 nt, which is the same as that corresponding to RNA from mitochondrial genes. This is evidence of a distinct viral RNA degradation mechanism active inside mitochondria that also may have an antiviral effect.IMPORTANCE This paper reports the first biological characterization of a bona fide plant mitovirus in an important crop, Chenopodium quinoa, providing data supporting that mitoviruses have the typical features of cryptic (persistent) plant viruses. We, for the first time, demonstrate that plant mitoviruses are associated with mitochondria in plants. In contrast to fungal mitoviruses, plant mitoviruses are not substantially affected by the antiviral silencing pathway, and the most abundant mitovirus small RNA length is 16 nt.
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Affiliation(s)
- L Nerva
- Institute for Sustainable Plant Protection, CNR, Turin, Italy
- Council for Agricultural Research and Economics-Research Centre for Viticulture and Enology CREA-VE, Conegliano, Italy
| | - G Vigani
- Plant Physiology Unit, Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - D Di Silvestre
- Institute for Biomedical Technology, CNR, Segrate, Milan, Italy
| | - M Ciuffo
- Institute for Sustainable Plant Protection, CNR, Turin, Italy
| | - M Forgia
- Institute for Sustainable Plant Protection, CNR, Turin, Italy
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - W Chitarra
- Institute for Sustainable Plant Protection, CNR, Turin, Italy
- Council for Agricultural Research and Economics-Research Centre for Viticulture and Enology CREA-VE, Conegliano, Italy
| | - M Turina
- Institute for Sustainable Plant Protection, CNR, Turin, Italy
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11
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Peyambari M, Warner S, Stoler N, Rainer D, Roossinck MJ. A 1,000-Year-Old RNA Virus. J Virol 2019; 93:e01188-18. [PMID: 30305356 PMCID: PMC6288340 DOI: 10.1128/jvi.01188-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 09/26/2018] [Indexed: 11/20/2022] Open
Abstract
Only a few RNA viruses have been discovered from archaeological samples, the oldest dating from about 750 years ago. Using ancient maize cobs from Antelope house, Arizona, dating from ca. 1,000 CE, we discovered a novel plant virus with a double-stranded RNA genome. The virus is a member of the family Chrysoviridae that infect plants and fungi in a persistent manner. The extracted double-stranded RNA from 312 maize cobs was converted to cDNA, and sequences were determined using an Illumina HiSeq 2000. Assembled contigs from many samples showed similarity to Anthurium mosaic-associated virus and Persea americana chrysovirus, putative species in the Chrysovirus genus, and nearly complete genomes were found in three ancient maize samples. We named this new virus Zea mays chrysovirus 1. Using specific primers, we were able to recover sequences of a closely related virus from modern maize and obtained the nearly complete sequences of the three genomic RNAs. Comparing the nucleotide sequences of the three genomic RNAs of the modern and ancient viruses showed 98, 96.7, and 97.4% identities, respectively. Hence, in 1,000 years of maize cultivation, this virus has undergone about 3% divergence.IMPORTANCE A virus related to plant chrysoviruses was found in numerous ancient samples of maize, with nearly complete genomes in three samples. The age of the ancient samples (i.e., about 1,000 years old) was confirmed by carbon dating. Chrysoviruses are persistent plant viruses. They infect their hosts from generation to generation by transmission through seeds and can remain in their hosts for very long time periods. When modern corn samples were analyzed, a closely related chrysovirus was found with only about 3% divergence from the ancient sequences. This virus represents the oldest known plant virus.
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Affiliation(s)
- Mahtab Peyambari
- Center for Infectious Disease Dynamics, Millennium Science Complex, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Sylvia Warner
- The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, USA
| | - Nicholas Stoler
- Center for Infectious Disease Dynamics, Millennium Science Complex, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Drew Rainer
- The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, USA
| | - Marilyn J Roossinck
- Center for Infectious Disease Dynamics, Millennium Science Complex, Pennsylvania State University, University Park, Pennsylvania, USA
- The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, USA
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12
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Ejmal MA, Holland DJ, MacDiarmid RM, Pearson MN. A novel chrysovirus from a clinical isolate of Aspergillus thermomutatus affects sporulation. PLoS One 2018; 13:e0209443. [PMID: 30571748 PMCID: PMC6301774 DOI: 10.1371/journal.pone.0209443] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 12/05/2018] [Indexed: 12/15/2022] Open
Abstract
A clinical isolate of Aspergillus thermomutatus (Teleomorph: Neosartorya pseudofischeri) was found to contain ~35 nm isometric virus-like particles associated with four double-stranded (ds) RNA segments, each of which coded for a single open reading frame. The longest dsRNA element (3589 nt) encodes a putative RNA-dependent RNA polymerase (1114 aa), the second longest dsRNA element (2772 nt) encodes a coat protein (825 aa), and the other two dsRNAs (2676 nt, 2514 nt) encode hypothetical proteins of 768 aa and 711 aa, respectively. Phylogenetic analysis of the amino acid sequences showed 41-60% similarity to the proteins coded by the dsRNAs of the most closely related virus, Penicillium janczewskii chrysovirus 2, indicating that it is a new species based on the International Committee on Taxonomy of Viruses criteria for the genus Chrysovirus. This is the first virus reported from A. thermomutatus and was tentatively named Aspergillus thermomutatus chrysovirus 1. A virus free line of the fungal isolate, cured by cycloheximide treatment, produced large numbers of conidia but no ascospores at both 20°C and 37°C, whereas the virus infected line produced ten-fold fewer conidia at 20°C and a large number of ascospores at both temperatures. The effects of the virus on fungal sporulation have interesting implications for the spread of the fungus and possible use of the virus as a biological control agent.
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Affiliation(s)
- Mahjoub A. Ejmal
- School of Biological Sciences, the University of Auckland, Auckland, New Zealand
| | - David J. Holland
- Infectious Diseases Unit, Division of Medicine, Staff Centre, Middlemore Hospital, Auckland, New Zealand
| | - Robin M. MacDiarmid
- School of Biological Sciences, the University of Auckland, Auckland, New Zealand
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Michael N. Pearson
- School of Biological Sciences, the University of Auckland, Auckland, New Zealand
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13
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Filloux D, Fernandez E, Comstock JC, Mollov D, Roumagnac P, Rott P. Viral Metagenomic-Based Screening of Sugarcane from Florida Reveals Occurrence of Six Sugarcane-Infecting Viruses and High Prevalence of Sugarcane yellow leaf virus. PLANT DISEASE 2018; 102:2317-2323. [PMID: 30207899 DOI: 10.1094/pdis-04-18-0581-re] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A viral metagenomics study of the sugarcane virome in Florida was carried out in 2013 to 2014 to analyze occurrence of known and potentially new viruses. In total, 214 sugarcane leaf samples were collected from different commercial sugarcane (Saccharum interspecific hybrids) fields in Florida and from other Saccharum and related species taken from two local germplasm collections. Virion-associated nucleic acids (VANA) metagenomics was used for detection and identification of viruses present within the collected leaf samples. VANA sequence reads were obtained for 204 leaf samples and all four previously reported sugarcane viruses occurring in Florida were detected: Sugarcane yellow leaf virus (SCYLV, 150 infected samples out of 204), Sugarcane mosaic virus (1 of 204), Sugarcane mild mosaic virus (13 of 204), and Sugarcane bacilliform virus (54 of 204). High prevalence of SCYLV in Florida commercial fields and germplasm collections was confirmed by reverse-transcription polymerase chain reaction. Sequence analyses revealed the presence of SCYLV isolates belonging to two different phylogenetic clades (I and II), including a new genotype of this virus. This viral metagenomics approach also resulted in the detection of a new sugarcane-infecting mastrevirus (recently described and named Sugarcane striate virus), and two potential new viruses in the genera Chrysovirus and Umbravirus.
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Affiliation(s)
- D Filloux
- CIRAD, BGPI, Montpellier, France, and BGPI, INRA, CIRAD, SupAgro, Univ Montpellier, Montpellier, France
| | - E Fernandez
- CIRAD, BGPI, Montpellier, France, and BGPI, INRA, CIRAD, SupAgro, Univ Montpellier, Montpellier, France
| | - J C Comstock
- Sugarcane Field Station, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Canal Point, FL 33438
| | - D Mollov
- USDA-ARS, National Germplasm Resources Laboratory, Beltsville, MD 20705
| | | | - P Rott
- University of Florida, Department of Plant Pathology, Everglades Research & Education Center, Belle Glade 33430
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14
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Zhai L, Zhang M, Hong N, Xiao F, Fu M, Xiang J, Wang G. Identification and Characterization of a Novel Hepta-Segmented dsRNA Virus From the Phytopathogenic Fungus Colletotrichum fructicola. Front Microbiol 2018; 9:754. [PMID: 29725323 PMCID: PMC5917037 DOI: 10.3389/fmicb.2018.00754] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 04/04/2018] [Indexed: 11/19/2022] Open
Abstract
A novel hepta-segmented double-stranded RNA (dsRNA) virus was isolated and characterized from the strain FJ-4 of the phytopathogenic fungus Colletotrichum fructicola, and was named Colletotrichum fructicola chrysovirus 1 (CfCV1). The full-length cDNAs of dsRNA1–7 were 3620, 2801, 2687, 2437, 1750, 1536, and 1211 bp, respectively. The 5′- and 3′-untranslated regions of the seven dsRNAs share highly similar internal sequence and contain conserved sequence stretches, indicating that they have a common virus origin. The 5′-and 3′-UTRs of the seven dsRNAs were predicted to fold into stable stem-loop structures. CfCV1 contains spherical virions that are 35 nm in diameter consisting of seven segments. The largest dsRNA of CfCV1 encodes an RNA-dependent RNA polymerase (RdRp), and the second dsRNA encodes a viral capsid protein (CP). The dsRNA5 encodes a C2H2-type zinc finger protein containing an R-rich region and a G-rich region. The smallest dsRNA is a satellite-like RNA. The functions of the other proteins encoded by dsRNA3, dsRNA4, dsRNA6 are unknown. Phylogenetic analysis, based on RdRp and CP, indicated that CfCV1 is phylogenetically related to Botryosphaeria dothidea chrysovirus 1 (BdCV1), and Penicillium janczewskii chrysovirus 2 (PjCV2), a cluster of an independent cluster II group in the family Chrysoviridae. Importantly, all the seven segments of CfCV1 were transmitted successfully to other virus-free strains with an all-or-none fashion. CfCV1 exerts minor influence on the growth of C. fructicola but can confer hypovirulence to the fungal host. To our knowledge, this is the first report of a hepta-segmented tentative chrysovirus in C. fructicola.
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Affiliation(s)
- Lifeng Zhai
- College of Life Science and Technology, Yangtze Normal University, Chongqing, China.,National Key Laboratory of Agromicrobiology, Huazhong Agricultural University, Wuhan, China
| | - Meixin Zhang
- College of Life Science and Technology, Yangtze Normal University, Chongqing, China.,National Key Laboratory of Agromicrobiology, Huazhong Agricultural University, Wuhan, China
| | - Ni Hong
- National Key Laboratory of Agromicrobiology, Huazhong Agricultural University, Wuhan, China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Feng Xiao
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Min Fu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jun Xiang
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Guoping Wang
- National Key Laboratory of Agromicrobiology, Huazhong Agricultural University, Wuhan, China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
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15
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Physiological traits of endornavirus-infected and endornavirus-free common bean (Phaseolus vulgaris) cv Black Turtle Soup. Arch Virol 2018; 163:1051-1056. [DOI: 10.1007/s00705-018-3702-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 11/25/2017] [Indexed: 11/26/2022]
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16
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Ghabrial SA, Castón JR, Coutts RHA, Hillman BI, Jiang D, Kim DH, Moriyama H, Ictv Report Consortium. ICTV Virus Taxonomy Profile: Chrysoviridae. J Gen Virol 2017; 99:19-20. [PMID: 29251589 PMCID: PMC5882088 DOI: 10.1099/jgv.0.000994] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The Chrysoviridae is a family of small, isometric, non-enveloped viruses (40 nm in diameter) with segmented dsRNA genomes (typically four segments). The genome segments are individually encapsidated and together comprise 11.5–12.8 kbp. The single genus Chrysovirus includes nine species. Chrysoviruses lack an extracellular phase to their life cycle; they are transmitted via intracellular routes within an individual during hyphal growth, in asexual or sexual spores, or between individuals via hyphal anastomosis. There are no known natural vectors for chrysoviruses. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Chrysoviridae, which is available at www.ictv.global/report/chrysoviridae.
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Affiliation(s)
- Said A Ghabrial
- Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, USA
| | - José R Castón
- Department of Structure of Macromolecules Centro Nacional Biotecnología/CSIC, Campus de Cantoblanco, 28049 Madrid, Spain
| | - Robert H A Coutts
- Department of Biological and Environmental Sciences, School of Life and Medical Sciences, University of Hertfordshire, Hatfield, AL10 9AB, UK
| | - Bradley I Hillman
- Department of Plant Biology and Pathology, School of Environmental and Biological Sciences Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Daohong Jiang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, PR China
| | - Dae-Hyun Kim
- Division of Biological Sciences, Chonbuk National University, Dukjindong 664-14, Jeonju, Chonbuk 561-756, Republic of Korea
| | - Hiromitsu Moriyama
- Laboratories of Molecular and Cellular Biology, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo 183-8509, Japan
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17
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Zhang J, Zhao Z, Hu R, Guo L, Zheng L, Du Z, Wu Z, Fang S, Zhang S, Liu Y. The genome sequence of Brassica campestris chrysovirus 1, a novel putative plant-infecting tripartite chrysovirus. Arch Virol 2016; 162:1107-1111. [PMID: 28004250 DOI: 10.1007/s00705-016-3196-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 12/07/2016] [Indexed: 11/25/2022]
Abstract
A putative chrysovirus recovered from Brassica campestris var. purpurea and provisionally named "Brassica campestris chrysovirus 1" (BrcCV1) was sequenced. The genome of the putative BrcCV1 consists of three double-stranded RNAs (dsRNAs) comprising 3,639 (dsRNA 1), 3,567 (dsRNA 2) and 3,337 (dsRNA 3) base pairs, respectively, each containing a single open reading frame (ORF 1-3). The putative proteins encoded by ORF 1-3 show homologies to RdRp, CP and chryso-P3 of approved or tentative chrysoviruses. In addition, the three dsRNAs of BrcCV1 contain highly conserved 5' and 3' untranslated regions (UTRs) in a way similar to known chrysoviruses. In a phylogenetic tree based on the conserved amino acid sequences of the RdRps of chrysoviruses, totiviruses and partitiviruses, the putative BrcCV1 formed a separate clade with Raphanus sativus chrysovirus 1 (RasCV1), a putative trisegmented, plant-infecting chrysovirus, in the family Chrysoviridae.
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Affiliation(s)
- Jun Zhang
- Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou, 434025, Hubei, China
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Zhonghao Zhao
- Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou, 434025, Hubei, China
- Hunan Plant Protection Institute, Changsha, 410125, Hunan, China
| | - Rong Hu
- Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Lingfang Guo
- College of Chemistry and environmental Engineering, Yangtze University, Jingzhou, 434023, Hubei, China
| | - Limin Zheng
- Hunan Plant Protection Institute, Changsha, 410125, Hunan, China
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Zhenguo Du
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Zujian Wu
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Shouguo Fang
- Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou, 434025, Hubei, China
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Songbai Zhang
- Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou, 434025, Hubei, China.
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, 434025, Hubei, China.
| | - Yong Liu
- Hunan Plant Protection Institute, Changsha, 410125, Hunan, China.
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18
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Molecular Characterization of a Trisegmented Mycovirus from the Plant Pathogenic Fungus Colletotrichum gloeosporioides. Viruses 2016; 8:v8100268. [PMID: 27690081 PMCID: PMC5086604 DOI: 10.3390/v8100268] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Revised: 09/15/2016] [Accepted: 09/19/2016] [Indexed: 01/26/2023] Open
Abstract
A novel double-stranded RNA (dsRNA) mycovirus, consisting of three dsRNA genome segments and possibly belonging to the family Chrysoviridae, was isolated from the filamentous phytopathogenic fungus Colletotrichum gloeosporioides and designated as Colletotrichum gloeosprioides chrysovirus 1 (CgCV1). The three dsRNAs of the CgCV1 genome with lengths of 3397, 2869, and 2630 bp (dsRNAs1–3) were found to contain a single open reading frame (ORF) putatively encoding the RNA-dependent RNA polymerase (RdRp), a capsid protein, and a protease, respectively, all of which exhibited some degree of sequence similarity to the comparable putative proteins encoded by the genus Chrysovirus. The 5′- and 3′-untranslated regions in each dsRNA segment contained similar sequences that were strictly conserved at the termini. Moreover, isometric virus-like particles (VLPs) with a diameter of approximately 40 nm were extracted from fungal mycelia. Phylogenetic analysis based on the conserved dsRNA1-encoded RdRp showed that CgCV1 is a new virus belonging to the Chrysoviridae family. BLAST analysis revealed the presence of CgCV1-like sequences in the chromosomes of Medicago truncatula and Solanum tuberosum. Moreover, some sequences in the transcriptome shotgun assembly (TSA) library and expressed sequence tag database (ESTdb) of other eudicot and monocot plants were also found to be related to CgCV1.
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19
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Kondo H, Hisano S, Chiba S, Maruyama K, Andika IB, Toyoda K, Fujimori F, Suzuki N. Reprint of "Sequence and phylogenetic analyses of novel totivirus-like double-stranded RNAs from field-collected powdery mildew fungi". Virus Res 2016; 219:39-50. [PMID: 27208846 DOI: 10.1016/j.virusres.2016.05.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 11/08/2015] [Accepted: 11/11/2015] [Indexed: 11/29/2022]
Abstract
The identification of mycoviruses contributes greatly to understanding of the diversity and evolutionary aspects of viruses. Powdery mildew fungi are important and widely studied obligate phytopathogenic agents, but there has been no report on mycoviruses infecting these fungi. In this study, we used a deep sequencing approach to analyze the double-stranded RNA (dsRNA) segments isolated from field-collected samples of powdery mildew fungus-infected red clover plants in Japan. Database searches identified the presence of at least ten totivirus (genus Totivirus)-like sequences, termed red clover powdery mildew-associated totiviruses (RPaTVs). The majority of these sequences shared moderate amino acid sequence identity with each other (<44%) and with other known totiviruses (<59%). Nine of these identified sequences (RPaTV1a, 1b and 2-8) resembled the genome of the prototype totivirus, Saccharomyces cerevisiae virus-L-A (ScV-L-A) in that they contained two overlapping open reading frames (ORFs) encoding a putative coat protein (CP) and an RNA dependent RNA polymerase (RdRp), while one sequence (RPaTV9) showed similarity to another totivirus, Ustilago maydis virus H1 (UmV-H1) that encodes a single polyprotein (CP-RdRp fusion). Similar to yeast totiviruses, each ScV-L-A-like RPaTV contains a -1 ribosomal frameshift site downstream of a predicted pseudoknot structure in the overlapping region of these ORFs, suggesting that the RdRp is translated as a CP-RdRp fusion. Moreover, several ScV-L-A-like sequences were also found by searches of the transcriptome shotgun assembly (TSA) libraries from rust fungi, plants and insects. Phylogenetic analyses show that nine ScV-L-A-like RPaTVs along with ScV-L-A-like sequences derived from TSA libraries are clustered with most established members of the genus Totivirus, while one RPaTV forms a new distinct clade with UmV-H1, possibly establishing an additional genus in the family. Taken together, our results indicate the presence of diverse, novel totiviruses in the powdery mildew fungus populations infecting red clover plants in the field.
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Affiliation(s)
- Hideki Kondo
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan.
| | - Sakae Hisano
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan
| | - Sotaro Chiba
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan
| | - Kazuyuki Maruyama
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan
| | - Ida Bagus Andika
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan
| | - Kazuhiro Toyoda
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Fumihiro Fujimori
- Department of Environmental Education, Tokyo Kasei University, 1-18-1 Kaga, Itabashi, Tokyo 173-8062, Japan
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan
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20
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Li L, Liu J, Zhang Q, Fu R, Zhu X, Li C, Chen J. Seed-borne viral dsRNA elements in three cultivatedRaphanusandBrassicaplants suggest three cryptoviruses. Can J Microbiol 2016; 62:287-95. [DOI: 10.1139/cjm-2015-0788] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Since the 1970s, several dsRNA viruses, including Radish yellow edge virus, Raphanus sativus virus 1, Raphanus sativus virus 2, and Raphanus sativus virus 3, have been identified and reported as infecting radish. In the present study, in conjunction with a survey of seed-borne viruses in cultivated Brassica and Raphanus using the dsRNA diagnostic method, we discovered 3 novel cryptoviruses that infect Brassica and Raphanus: Raphanus sativus partitivirus 1, which infects radish (Raphanus sativus); Sinapis alba cryptic virus 1, which infects Sinapis alba; and Brassica rapa cryptic virus 1 (BrCV1), which infects Brassica rapa. The genomic organization of these cryptoviruses was analyzed and characterized. BrCV1 might represent the first plant partitivirus found in Gammapartitivirus. Additionally, the evolutionary relationships among all of the partitiviruses reported in Raphanus and Brassica were analyzed.
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Affiliation(s)
- Liqiang Li
- College of Life Science, Zhejiang University, Hangzhou, 310058, People’s Republic of China
| | - Jianning Liu
- Institute of Bioengineering, Zhejiang Sci-Tech University, Hangzhou, 310018, People’s Republic of China
| | - Qiong Zhang
- Institute of Bioengineering, Zhejiang Sci-Tech University, Hangzhou, 310018, People’s Republic of China
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, People’s Republic of China
| | - Runying Fu
- Shenzhen Seventh People’s Hospital, Shenzhen, 518081, People’s Republic of China
| | - Xiwu Zhu
- Institute of Bioengineering, Zhejiang Sci-Tech University, Hangzhou, 310018, People’s Republic of China
- Institute of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi, 41700, People’s Republic of China
| | - Chao Li
- College of Life Science, Shenzhen University, Shenzhen, 518068, People’s Republic of China
| | - Jishuang Chen
- College of Life Science, Zhejiang University, Hangzhou, 310058, People’s Republic of China
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, People’s Republic of China
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21
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Kondo H, Hisano S, Chiba S, Maruyama K, Andika IB, Toyoda K, Fujimori F, Suzuki N. Sequence and phylogenetic analyses of novel totivirus-like double-stranded RNAs from field-collected powdery mildew fungi. Virus Res 2015; 213:353-364. [PMID: 26592174 DOI: 10.1016/j.virusres.2015.11.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 11/08/2015] [Accepted: 11/11/2015] [Indexed: 11/30/2022]
Abstract
The identification of mycoviruses contributes greatly to understanding of the diversity and evolutionary aspects of viruses. Powdery mildew fungi are important and widely studied obligate phytopathogenic agents, but there has been no report on mycoviruses infecting these fungi. In this study, we used a deep sequencing approach to analyze the double-stranded RNA (dsRNA) segments isolated from field-collected samples of powdery mildew fungus-infected red clover plants in Japan. Database searches identified the presence of at least ten totivirus (genus Totivirus)-like sequences, termed red clover powdery mildew-associated totiviruses (RPaTVs). The majority of these sequences shared moderate amino acid sequence identity with each other (<44%) and with other known totiviruses (<59%). Nine of these identified sequences (RPaTV1a, 1b and 2-8) resembled the genome of the prototype totivirus, Saccharomyces cerevisiae virus-L-A (ScV-L-A) in that they contained two overlapping open reading frames (ORFs) encoding a putative coat protein (CP) and an RNA dependent RNA polymerase (RdRp), while one sequence (RPaTV9) showed similarity to another totivirus, Ustilago maydis virus H1 (UmV-H1) that encodes a single polyprotein (CP-RdRp fusion). Similar to yeast totiviruses, each ScV-L-A-like RPaTV contains a -1 ribosomal frameshift site downstream of a predicted pseudoknot structure in the overlapping region of these ORFs, suggesting that the RdRp is translated as a CP-RdRp fusion. Moreover, several ScV-L-A-like sequences were also found by searches of the transcriptome shotgun assembly (TSA) libraries from rust fungi, plants and insects. Phylogenetic analyses show that nine ScV-L-A-like RPaTVs along with ScV-L-A-like sequences derived from TSA libraries are clustered with most established members of the genus Totivirus, while one RPaTV forms a new distinct clade with UmV-H1, possibly establishing an additional genus in the family. Taken together, our results indicate the presence of diverse, novel totiviruses in the powdery mildew fungus populations infecting red clover plants in the field.
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Affiliation(s)
- Hideki Kondo
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan.
| | - Sakae Hisano
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan
| | - Sotaro Chiba
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan
| | - Kazuyuki Maruyama
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan
| | - Ida Bagus Andika
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan
| | - Kazuhiro Toyoda
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Fumihiro Fujimori
- Department of Environmental Education, Tokyo Kasei University, 1-18-1 Kaga, Itabashi, Tokyo 173-8062, Japan
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan
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22
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Ghabrial SA, Castón JR, Jiang D, Nibert ML, Suzuki N. 50-plus years of fungal viruses. Virology 2015; 479-480:356-68. [PMID: 25771805 DOI: 10.1016/j.virol.2015.02.034] [Citation(s) in RCA: 454] [Impact Index Per Article: 50.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 01/31/2015] [Accepted: 02/19/2015] [Indexed: 10/23/2022]
Abstract
Mycoviruses are widespread in all major taxa of fungi. They are transmitted intracellularly during cell division, sporogenesis, and/or cell-to-cell fusion (hyphal anastomosis), and thus their life cycles generally lack an extracellular phase. Their natural host ranges are limited to individuals within the same or closely related vegetative compatibility groups, although recent advances have established expanded experimental host ranges for some mycoviruses. Most known mycoviruses have dsRNA genomes packaged in isometric particles, but an increasing number of positive- or negative-strand ssRNA and ssDNA viruses have been isolated and characterized. Although many mycoviruses do not have marked effects on their hosts, those that reduce the virulence of their phytopathogenic fungal hosts are of considerable interest for development of novel biocontrol strategies. Mycoviruses that infect endophytic fungi and those that encode killer toxins are also of special interest. Structural analyses of mycoviruses have promoted better understanding of virus assembly, function, and evolution.
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Affiliation(s)
- Said A Ghabrial
- Plant Pathology Department, University of Kentucky, Lexington, KY, USA.
| | - José R Castón
- Department of Structure of Macromolecules, Centro Nacional Biotecnologıa/CSIC, Campus de Cantoblanco, Madrid, Spain
| | - Daohong Jiang
- State Key Lab of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, PR China
| | - Max L Nibert
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
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23
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Roossinck MJ. Metagenomics of plant and fungal viruses reveals an abundance of persistent lifestyles. Front Microbiol 2015; 5:767. [PMID: 25628611 PMCID: PMC4290624 DOI: 10.3389/fmicb.2014.00767] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 12/16/2014] [Indexed: 02/01/2023] Open
Affiliation(s)
- Marilyn J Roossinck
- Department of Plant Pathology and Environmental Microbiology, Center for Infectious Disease Dynamics, Pennsylvania State University University Park, PA, USA
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24
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A dsRNA mycovirus, Magnaporthe oryzae chrysovirus 1-B, suppresses vegetative growth and development of the rice blast fungus. Virology 2014; 448:265-73. [DOI: 10.1016/j.virol.2013.10.022] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 08/26/2013] [Accepted: 10/15/2013] [Indexed: 11/20/2022]
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Abstract
Most of reported fungal viruses (mycoviruses) have double-stranded RNA (dsRNA) genomes. This may reflect the simple, easy method for mycovirus hunting that entails detection of dsRNAs as a sign of viral infections. There are an increasing number of screens of various fungi, particularly phytopathogenic fungi for viruses pathogenic to host fungi or able to confer hypovirulence to them. This bases on an attractive research field of biological control of fungal plant diseases using viruses (virocontrol), mainly targeting important phytopathogenic fungi. While isolated viruses usually induce asymptomatic symptoms, they show a considerably high level of diversity. As of 2014, fungal dsRNA viruses are classified into six families: Reoviridae, Totiviridae, Chrysoviridae, Partitiviridae, Megabirnaviridae and Quadriviridae. These exclude unassigned mycoviruses which will definitely be placed into distinct families and/or genera. In this review article, dsRNA viruses isolated from the kingdom Fungi including as-yet-unclassified taxa are overviewed. Some recent achievements in the related field are briefly introduced as well.
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